Ultimately, a question like this boils down to how much you value balance. SE can theoretically offer customization (though none of the FF titles have featured much of it; in many ways, they shouldn't even properly be called RPGs), but doing so will guarantee that a degree of balance is sacrificed.
Personally, I'd rather see the customization. FFXIV is balanced almost to a fault - and the benefits don't outweigh the costs, in my opinion. I'd like to see skill trees, ideally, but I doubt both SE's motivation and ability to actually implement such a large change successfully. More realistically, I think a more carefully developed Merit system would be a fine addition to the title. I'm also surprised they haven't capitalized on Materia more; certainly a Magian-style system for collections of Materia that can be infused (and removed) in any gear could go a long way. For instance, for a Healer-style job, you could have Materia branches that focus on Spell Speed, add a small AoE effect onto single-target spells, improve MP maintenance, maybe add a small Stoneskin effect to cures (like Afflatus Solace in FFXI). These branches could be leveled via a Magian-like grind, and maybe inserted into, say, a body piece. The trick of this would be making sure that the paths offer meaningful, useful changes to how a job plays, without any one path being a clear-cut winner. Of course, another important piece here is, players would have to be limited to at most one of these types of Materia per job.
As an aside, while I admittedly haven't read the entire thread, I think the idea of simply opening up existing abilities would be a huge mistake. There are two large weaknesses here.
Firstly, far from adding customization, such a system would undoubtedly lead to more "required abilities" for people to be accepted in groups. I suspect there would quickly be a list of "best" abilities hashed out, which 90+% of people use, thereby eliminating the feel of customization. It would also cause more balance issues than it's worth. Customization options should most likely focus on allowing a player to shape how they play a predefined role, rather than allowing the role itself to dramatically change. For instance, DD should be able to customize how they deal damage, but they shouldn't be able to transform themselves into half-arsed healers or tanks (as an example).
Secondly, such a change would have an uneven impact in terms of how much time investment was required by a player. Individuals with everything at level 50 could take advantage of loosened restrictions the second they log on, whereas new players starting would have an (increasingly large) amount of leveling to do before they began to realize the full effects. I don't think that fits very well with the spirit of FFXIV.
Just my two gil, anyway.